3-48190429-T-G

Variant names:

• chr3-48190429-T-G
• rs1903061

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.931 in 152,018 control chromosomes in the GnomAD database, including 66,004 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.93 (66004 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141356 AN: 151900 Hom.: 65947 Cov.: 29

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.932

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.931 AC: 141472 AN: 152018 Hom.: 66004 Cov.: 29 AF XY: 0.930 AC XY: 69093 AN XY: 74264

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.933

Alfa AF: 0.902 Hom.: 4134

Bravo AF: 0.941

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1903061; hg19: chr3-48231919;